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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · Jul 27

This was great team science and many thanks are also due to @danielleingle.bsky.social @ellarodwell.bsky.social @charlotteechong.bsky.social @malakades.bsky.social, @jayhinton.bsky.social and @neilhall.bsky.social of Salmonella10k, @mariechattaway.bsky.social Ben Howden, Deb Williamson and more!

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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · Jul 27

Massive thanks to the phenomenal co-first authors @1caiseypulford and @blancaps.bsky.social‬ and especially to one of my favourite scientists to work with, co-corresponding author and fellow history fanatic @weill_xavier 10/n

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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · Jul 27

So, welcome to your new genomic understanding of S. Panama and please go ahead and check out the data yourselves on the associated ‪@microreact.bsky.social‬ page! microreact.org/project/span... 9/n

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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · Jul 27

As a final analysis we compared the predicted invasiveness of S. Panama with other broad and narrow host range serovars and found it was comparable to other major causes of iNTS (thanks to @nwheeler443.bsky.social‬ for the ML classifier to do so) 8/n

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Kate Baker @ksbakes.bsky.social · Jul 27

Temporal analysis revealed that the four major clades all emerged in the late 1800s, coincident with European efforts to build the Panama canal (‘Panama Fever’ by ‪@matthewparker70.bsky.social‬ is recommended reading for those with an interest in the history here) 7/n

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Kate Baker @ksbakes.bsky.social · Jul 27

We also found multidrug resistance cassettes; fluoroquinolone resistance (bumping S. Panama onto the WHO AMR priority pathogens list); and a single extensively drug-resistant isolate 6/n

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Kate Baker @ksbakes.bsky.social · Jul 27

Although antimicrobial resistance (AMR) levels were low overall (14% of isolates), resistant isolates were predominately found in Clade 2 (European-associated) and Clade 4 (associated with Oceania and Asia) 5/n

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Kate Baker @ksbakes.bsky.social · Jul 27

Population structure analyses revealed the presence of four major Clades that had significant geographic associations 4/n

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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · Jul 27

To better characterise S. Panama we sequenced a global collection of isolates (n=731) from public health surveillance datasets from @ukhsa.bsky.social‬ @thedohertyinst.bsky.social‬, historical collections from ‪@pasteur.fr‬ and publicly available data (n=105) from 1931 to 2019 3/n

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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · Jul 27

S. Panama causes major disease concerns, including high rates of iNTS in French Guiana, large outbreaks in European pork, AMR in Asia, and outbreaks in American soldiers from where the first (extant) isolate from 1931 came from (More in our 2019 review: 10.1128/IAI.00273-19) 2/n

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Dr Blanca Perez-Sepulveda @blancaps.bsky.social · Aug 1

Finally out!! It was a long time in the making, I hope you enjoy it!! #salmonella #iNTS #AMR

Kate Baker @ksbakes.bsky.social · Jul 27

There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n

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Dr Blanca Perez-Sepulveda @blancaps.bsky.social · May 20

Great work led by the talented @edcoakes.bsky.social!!

University of Liverpool News @livuninews.bsky.social · May 20

NEWS | A study has advanced how we diagnose the causes of diarrhoeal illness.

Researchers used cutting-edge techniques to examine DNA & RNA directly from samples—no need to grow bugs in a lab! This reveals emerging pathogens that traditional tests can miss ⬇️

news.liverpool.ac.uk/2025/05/20/a...

News: study improves detection of hard-to-find diarrhoeal infections

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Dr Blanca Perez-Sepulveda @blancaps.bsky.social · May 20

Our paper is out!! Take a look at this comprehensive 🧵 by @edcoakes.bsky.social, one of the most talented and persistent scientists I work with

Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

1/12 🎉 We're excited to announce our Genome Medicine paper benchmarking 1000+ metagenomes (DNA) and metatranscriptomes (RNA) from infectious intestinal disease patients against pathogen diagnostics. The full dataset is public to accelerate pathogen discovery & surveillance: doi.org/10.1186/s130...

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

12/12 📰 For more background and wider context, check out the @liverpooluni.bsky.social press release covering this study’s impact on understanding and diagnosing infectious intestinal diseases: news.liverpool.ac.uk/2025/05/20/a...

Advanced genomics study improves detection of hard-to-find diarrhoeal infections - University of Liverpool News

Advanced genomics study improves detection of hard-to-find diarrhoeal infections

news.liverpool.ac.uk

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

11/12 🙏 A big thank you to all my amazing collaborators who made this work possible @blancaps.bsky.social @jayhinton.bsky.social @acdarby.bsky.social (PI) and many of the INTEGRATE consortium not on BlueSky.
Thank you to @nihr.bsky.social for funding via the second HPRU-GI @livuni-ives.bsky.social.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

9/12 📊 RNA/DNA ratios differed significantly between positive and negative cases, helping distinguish true infection from bystander carriage and providing a molecular readout of microbial activity.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

8/12 📦 Critically, RNA in stool remained stable enough for pathogen detection without preservatives (and after self-sample and surviving the mail service!), providing evidence for the routine potential of metatranscriptomics in clinical settings (with some work!)

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

7/12 🧫 For the first time, we captured a comprehensive snapshot of Salmonella gene expression from a human stool sample. These data reveal how bacteria survive and adapt after leaving the gut. Explore via Hinton Lab’s interactive browser: jb.hintonlab.com/index.html?d...

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

6/12 🦠➡️🧬 Metatranscriptomics also detected Cryptosporidium via its RNA virus, CSpV1, previously reported in diarrhoeic animals (doi.org/10.1186/s135...). Cryptosporidium was undetectable in metagenomic data, suggesting RNA sequencing can sensitively detect it when DNA methods fall short.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

5/12 🦠 Metatranscriptomics captured active Adenovirus F infections via broad transcriptome coverage (in a couple of samples, near complete!), despite it being a DNA virus, highlighting its use in profiling ongoing viral activity during diarrhoeal illness.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

4/12
🧪 Metatranscriptomics showed superior sensitivity, with strong correlation to conventional diagnostics for 6/15 pathogens and to Luminex for 8/14.
🧬 Metagenomics performed well for some targets but showed lower overall concordance.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

🔬 3/12 As a part of the INTEGRATE study, we sequenced stool from 1,067 patients using both metagenomics and metatranscriptomics. We identified pathogens in these data and benchmarked against routine diagnostics and Luminex xTAG GPP, a multiplex test for key bacterial, viral, and parasitic pathogens.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

2/12 💩 Diarrhoea affects ~18 million annually in the UK, yet traditional diagnostics often miss causes, especially hard-to-culture or emerging pathogens. Our work shows how next-generation sequencing can transform the detection and understanding of GI infections.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

1/12 🎉 We're excited to announce our Genome Medicine paper benchmarking 1000+ metagenomes (DNA) and metatranscriptomes (RNA) from infectious intestinal disease patients against pathogen diagnostics. The full dataset is public to accelerate pathogen discovery & surveillance: doi.org/10.1186/s130...

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Reposted by Dr Blanca Perez-Sepulveda

Evelien Adriaenssens @evelienadri.bsky.social · Apr 16

Absolutely love this new publication by my colleagues @blancaps.bsky.social & @emmabeansworth.bsky.social

We need to foster an inclusive research culture with diverse representation to tackle global issues now and in future.

www.nature.com/articles/s44...

Importance of diversity and representation in science: benefits towards strengthening our response to global challenges - npj Antimicrobials and Resistance

Diversity is a mechanism that pathogens use to adapt and survive new challenges, like the introduction of antimicrobials in modern medicine. With antimicrobial resistance increasing and antibiotic dev...

www.nature.com

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